It is, as Austinstar says, very difficult to judge between different sciences, and it's also difficult to judge between eras - some of the ancient Greeks had astonishingly far reaching ideas, but lacked the equipment to test them. And today scientists may be just as brilliant as any in history, but such is the complexity of science that it is difficult for an individual to make a stand-out discovery - great achievements today usually come through teams of specialists each playing their part. Perhaps the scientists of 150-300 years ago were the lucky ones; with the recent invention of telescopes and microscopes, and then the industrial revolution, it was possible for bright thinkers to make truly revelatory discoveries in one field, or else major contributions across many fields.
However, my 'favourites' are most probably Archimedes, Galileo, Huygens, Newton and my own personal hero - Charles Darwin. Also Isembard Kingdom Brunel, if one can describe him as a scientist rather than an engineer.
I'm glad you've asked this question quicksand, because the work of such people ashould be highlighted. I've written a page about one of these men - Huygens - and also a page about the great Egyptian polymath, Imhotep, and intend to write about many others, because too many of the greatest brains in history are too little understood or appreciated for what they achieved. Hopefully some more hubbers will answer your question - It would be nice to see further ideas on this, and the reasons which people give for their choice.